README.md

In wf-frank2019/ne.PCA: The node and edge Prioritization based Community Analysis framework

COMMUNITY DETECTION

The node and edge Prioritization based Community Analysis (ne.PCA) for Protein-Protein Interaction Network😊

Usage

# version 3.6.0 for check
# install.packages("devtools")
library(devtools)
devtools::install_github("wf-frank2019/ne.PCA")
library(ne.PCA)
# ? or help(" ") for description of five functions：qc.DEGs();RWRs.CN();TFCs();MODULEs();ne.PCA()

# If you wanna identify key biological network nodes or edges or modules as well as drugability prediction, just type：
ne.PCA(nodes,edges)

Overall Presentation

NSCLC for example

ref: https://www.mdpi.com/2073-4409/10/2/402

1 Preliminary omics research

DEGs were identified respectively:588 common DEGs

2 NSCLC seed genes collection

NSCLC seed genes were collected from seven database with different focus

details:

DisGeNet(http://www.disgenet.org/downloads) Pinero J, Ramirez-Anguita JM, Sauch-Pitarch J et al. The DisGeNET knowledge platform for disease genomics: 2019 update,NU-CLEIC ACIDS RESEARCH 2020.

KEGG(https://www.kegg.jp/kegg/) Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes,NUCLEIC ACIDS RESEARCH 2000.

Cancer Gene Census(https://cancer.sanger.ac.uk/census) Sondka,Z.,Bamford, S.,Cole,C.G.et al.The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers,Nat Rev Cancer 2018.

OMIM(https://www.omim.org/downloads) Amberger JS, Bocchini CA, Scott AF, Hamosh A. OMIM.org: leveraging knowledge across phenotype-gene relationships,Nucleic Acids Res 2019.

Diseases(https://diseases.jensenlab.org/Downloads) Pletscher-Frankild S, Pallejà, Albert, Tsafou K, et al. DISEASES: Text mining and data integration of disease–gene associations,Methods 2015.

IntAct(https://www.ebi.ac.uk/intact/downloads) Orchard S1, Ammari M, Aranda B, et al. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases,Nucleic Acids Research 2014.

OncoPPI(http://oncoppi.emory.edu) Li,Z.,Ivanov,A.,Su,R.et al.The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies,Nat Commun 2017.

3 PPIN Construction

Protein-protein interaction network based on STRING(https://string-db.org/)
DEGs include 12 known genes from KEGG(https://www.kegg.jp/kegg/),COSMIC(https://cancer.sanger.ac.uk/cosmic/),DisGenet(https://www.disgenet.org/)
KeyNetwork：nodes and edges are weighted by RWRscore and TFscore respectively

4 Communities

Community Network Overview

wf-frank2019/ne.PCA documentation built on May 4, 2022, 4:47 p.m.